Nucleic acid sequences encoding transcription factors regulating alkaloid biosynthesis and their use in modifying plant metabolism

ABSTRACT

Plant metabolism and alkaloid levels can be regulated by transcription factors that regulate the nicotinic alkaloid biosynthetic pathway. In one embodiment, the disclosure provides a transcription factor that negatively regulates alkaloid biosynthesis, such as nicotine biosynthesis.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.14/261,240, filed Apr. 24, 2014, which is a divisional of U.S. patentapplication Ser. No. 12/601,752, filed Mar. 1, 2010, which is the U.S.National Phase of International Patent Application No.PCT/IB2008/003131, filed May 23, 2008, which claims priority from U.S.Provisional Patent Application No. 60/924,675, filed May 25, 2007. Thecontents of these applications are incorporated herein by reference intheir entirety.

FIELD OF THE INVENTION

The present invention is related to transcription factors for modifyingplant metabolism, and to nucleic acid molecules that encode suchtranscription factors. The invention relates, inter alia, to nucleicacid sequences that encode transcription factors that regulate alkaloidproduction in plants, particularly but not exclusively nicotinicalkaloid production in a tobacco plant, and for producing plants andcells with altered alkaloid content.

BACKGROUND OF THE INVENTION

Many plant natural products have biological activities that make themvaluable as pharmaceutical drugs. Alkaloids are a class of naturalproducts that have proved particularly useful as drugs and medicines.Examples of biologically-active alkaloids include morphine, scopolamine,camptothecin, cocaine and nicotine. These compounds are all isolatedfrom plant sources for use as pharmaceutical drugs. Nicotine, morphine(and related opiates) and cocaine are also addictive drugs that areresponsible for significant health and societal problems worldwide.

Nicotine is a pyrrolidine alkaloid that exhibits a range ofbioactivities, including potent toxicity and nervous system stimulation.In Nicotiana tabacum, N. benthamiana and a number of other species,nicotine is synthesized in the roots and then transported to the leaves,where it appears to play a role in defense. The biosynthesis of nicotineand many other plant metabolites can be induced by the application of aclass of volatile plant hormones collectively termed jasmonates(Gundlach et al., Proc. Natl. Acad. Sci. U.S.A. 89: 2389-2393 (1992)).Although increases in nicotine levels can be induced by wounding orjasmonate application, the actual regulatory machinery responsible forthis induction has yet to be discovered.

Plant natural product biosynthesis is mainly under transcriptionalcontrol, which allows plants to regulate metabolism in a developmentaland stress-specific fashion. A number of transcription factors thatregulate specific branches of secondary metabolism have been identifiedin plants. Anthocyanin biosynthesis is controlled by interacting MYBproteins (e.g. maize C1, Arabidopsis PAP1/PAP2) andbasic-helix-loop-helix proteins (e.g. maize R, petunia AN1) (for areview see Vom Endt et al., Phytochemistry 61: 107-114 (2002)). Examplesof other transcription factors regulating plant metabolic processesinclude a WRKY-type transcription factor that appears to control thetranscription of a sesquiterpene synthase in cotton trichomes (Xu etal., Plant Physiol. 135: 507-515 (2004)) and an AP2/ERF-liketranscription factor, WIN1, that up-regulates wax biosynthesis inArabidopsis (Broun et al., Curr. Opin. Plant Biol. 7: 202-209 (2004)).

Overexpression of ORCA3 in Catharanthus roseus cell suspensionsincreased levels of transcripts of genes encoding some of the enzymes inthe C. roseus terpenoid indole alkaloid pathway, but alkaloidaccumulation was observed only when the cell suspension were providedwith loganin, a terpenoid precursor. (van der Fits and Memelink. Science289:295-297 (2000)). Overexpression of two transcription factors, NtORC1and NtJAP1, increased transient expression of marker genes linked to aputrescine N-methyltransferase (PMT) promoter in tobacco cellsuspensions. (De Sutter et al., Plant J. 44:1065-76 (2005))

SUMMARY OF THE INVENTION

In one aspect, the invention provides an isolated nucleic acid moleculecomprising a nucleotide sequence selected from the group consistingof:(a) a nucleotide sequence set forth in SEQ ID NO: 1, SEQ ID NO: 2,SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 9,SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 14 or SEQ ID NO: 15; (b) anucleotide sequence that encodes a polypeptide having the amino acidsequence set forth in SEQ ID NO: 3, SEQ ID NO: 7, SEQ ID NO: 10, SEQ IDNO: 13 or SEQ ID NO: 16; c) a nucleotide sequence that is at least 90%identical to the nucleotide sequences of (a) or (b), and encodes atranscription factor that regulates alkaloid biosynthesis; and (d) anucleotide sequence that hybridizes under stringent conditions to thenucleotide sequences of (a), (b), or (c), and encodes a transcriptionfactor that regulates alkaloid biosynthesis.

In one embodiment, there is provided a genetically engineered plant cellcomprising at least 21 consecutive nucleotides of the nucleic acidsequence, wherein said consecutive nucleotides are in either sense orantisense orientation. In a further embodiment, a plant comprises theplant cell. In another further embodiment, a tissue culture comprisesthe plant cell, wherein said culture has enhanced production orsecretion of an at least one alkaloid, alkaloid precursor, or alkaloidanalog. In a further embodiment, there is a method for producing analkaloid, alkaloid precursor, or alkaloid analog, comprising isolatingsaid alkaloid, alkaloid precursor, alkaloid analog from the tissueculture. In one further embodiment, the tissue culture comprises a cellof a Nicotiana plant, such as Nicotiana tabacum.

In another aspect, the invention provides a recombinant transcriptionfactor that regulates alkaloid biosynthesis having an amino acidsequence selected from the group consisting of: (a) an amino acidsequence set forth in SEQ ID NO: 3, SEQ ID NO: 7, SEQ ID NO: 10, SEQ IDNO: 13, or SEQ ID NO: 16; and (b) a variant of an amino acid sequenceset forth in (a). In one embodiment, the alkaloid is a nicotinicalkaloid. In a further embodiment, the nicotinic alkaloid is nicotine.In another embodiment, the plant belongs to the genus Nicotiana. In afurther embodiment, the plant is Nicotiana tabacum. In anotherembodiment, the method provides a reduced alkaloid plant. In a furtherembodiment, a reduced alkaloid product is produced from the reducedalkaloid plant.

In another aspect, there is provided a method for reducing an alkaloidin a plant, comprising down-regulating a transcription factor thatpositively regulates alkaloid biosynthesis. In one embodiment, thetranscription factor is down-regulated by (a) introducing into the planta nucleotide sequence comprising i) at least 21 consecutive nucleotidesof a sequence selected from the group of SEQ ID NO: 1, SEQ ID NO: 5, SEQID NO: 8, or SEQ ID NO: 11, wherein said consecutive nucleotides are ineither sense or antisense orientation; and (b) growing the plant underconditions whereby said nucleotide sequence decreases levels of thetranscription factor in the plant compared to a control plant grownunder similar conditions. In one embodiment, the alkaloid is a nicotinicalkaloid. In a further embodiment, the nicotinic alkaloid is nicotine.In another embodiment, the plant belongs to the genus Nicotiana. In afurther embodiment, the plant is Nicotiana tabacum. In anotherembodiment, the method provides a reduced alkaloid plant. In a furtherembodiment, a reduced alkaloid product is produced from the reducedalkaloid plant.

In another aspect, the invention provides a method for reducing alkaloidlevels in a population of plants, comprising: (a) providing a populationof mutated plants; (b) detecting and selecting a target mutated plantwithin said population, wherein said target mutated plant has decreasedexpression of a transcription factor that positively regulates alkaloidbiosynthesis compared to a control plant; and (c) selectively breedingthe target mutated plant to produce a population of plants havingdecreased expression of a transcription factor that positively regulatesalkaloid biosynthesis compared to a population of control plants. In oneembodiment, the detecting comprises using primers developed from SEQ IDNO: 1, SEQ ID NO: 5, SEQ ID NO: 8, or SEQ ID NO: 11 to amplify regionsof the transcription factor gene from mutated plants in the populationof mutated plants, identifying mismatches between the amplified regionsand corresponding regions in wild-type gene that lead to the decreasedexpression of a transcription factor that positively regulates alkaloidbiosynthesis, and identifying the mutated plant that contains themismatches. In one embodiment, the alkaloid is a nicotinic alkaloid. Ina further embodiment, the nicotinic alkaloid is nicotine. In anotherembodiment, the plant belongs to the genus Nicotiana. In a furtherembodiment, the plant is Nicotiana tabacum. In another embodiment, themethod provides a reduced alkaloid plant. In a further embodiment, areduced alkaloid product is produced from the reduced alkaloid plant.

In another aspect, the invention provides a method for reducing analkaloid in a plant, comprising up-regulating a transcription factorthat negatively regulates alkaloid biosynthesis. In one embodiment, thetranscription factor is up-regulated by (a) introducing into the plantan expression construct comprising a nucleotide sequence selected fromthe group of SEQ ID NO: 4, SEQ ID NO: 14, or SEQ ID NO: 15; and (b)growing the plant under conditions whereby said expression constructincreases levels of the transcription factor in the plant compared to acontrol plant grown under similar conditions. In one embodiment, thealkaloid is a nicotinic alkaloid. In a further embodiment, the nicotinicalkaloid is nicotine. In another embodiment, the plant belongs to thegenus Nicotiana. In a further embodiment, the plant is Nicotianatabacum. In another embodiment, the method provides a reduced alkaloidplant. In a further embodiment, a reduced alkaloid product is producedfrom the reduced alkaloid plant.

In another aspect, the invention provides a method for reducing anicotinic alkaloid in a plant, comprising down-regulating atranscription factor that positively regulates alkaloid biosynthesis anddown-regulating at least one of NBB1, A622, QPT, PMT, and MPO. In oneembodiment, the nicotinic alkaloid is nicotine. In another embodiment,the plant belongs to the genus Nicotiana. In a further embodiment, theplant is Nicotiana tabacum. In another embodiment, the method provides areduced alkaloid plant. In a further embodiment, a reduced alkaloidproduct is produced from the reduced alkaloid plant.

In another aspect, the invention provides a method for reducing anicotinic alkaloid in a plant, comprising up-regulating a transcriptionfactor that negatively regulates alkaloid biosynthesis anddown-regulating at least one of NBB1, A622, QPT, PMT, and MPO. In oneembodiment, the nicotinic alkaloid is nicotine. In another embodiment,the plant belongs to the genus Nicotiana. In a further embodiment, theplant is Nicotiana tabacum. In another embodiment, the method provides areduced alkaloid plant. In a further embodiment, a reduced alkaloidproduct is produced from the reduced alkaloid plant.

In another aspect, the invention provides a method for increasing analkaloid in a plant, comprising down-regulating a transcription factorthat negatively regulates alkaloid biosynthesis. In one embodiment, thetranscription factor is down-regulated by (a) introducing into the planta nucleotide sequence comprising i) at least 21 consecutive nucleotidesof a sequence selected from the group of SEQ ID NO: 4 and SEQ ID NO: 14,wherein said consecutive nucleotides are in either sense or antisenseorientation; and (b) growing the plant under conditions whereby saidnucleotide sequence decreases levels of the transcription factor in theplant compared to a control plant grown under similar conditions. In oneembodiment, the alkaloid is a nicotinic alkaloid. In another embodiment,the plant belongs to the genus Nicotiana. In a further embodiment, theplant is Nicotiana tabacum. In another embodiment, the method producesan increased alkaloid plant. In a further embodiment, an increasedalkaloid product is produced from the plant. In a still furtherembodiment, the increased alkaloid is nicotine.

In another aspect, the invention provides a method for increasingalkaloid levels in a population of plants, comprising: (a) providing apopulation of mutated plants; (b) detecting and selecting a targetmutated plant within said population, wherein said target mutated planthas decreased expression of a transcription factor that negativelyregulates alkaloid biosynthesis compared to a control plant; and (c)selectively breeding the target mutated plant to produce a population ofplants having decreased expression of a transcription factor thatnegatively regulates alkaloid biosynthesis compared to a population ofcontrol plants. In one embodiment, the detecting comprising usingprimers developed from SEQ ID NO: 4 or SEQ ID NO: 14 to amplify regionsof the transcription factor gene from mutated plants in the populationof mutated plants, identifying mismatches between the amplified regionsand corresponding regions in wild-type gene that lead to the decreasedexpression of a transcription factor that negatively regulates alkaloidbiosynthesis, and identifying the mutated plant that contains themismatches. In one embodiment, the alkaloid is a nicotinic alkaloid. Inanother embodiment, the plant belongs to the genus Nicotiana. In afurther embodiment, the plant is Nicotiana tabacum. In anotherembodiment, the method produces an increased alkaloid plant. In afurther embodiment, an increased alkaloid product is produced from theplant. In a still further embodiment, the increased alkaloid isnicotine.

In another aspect, the invention provides a method for increasing analkaloid in a plant, comprising up-regulating a transcription factorthat positively regulates alkaloid biosynthesis. In one embodiment, thetranscription factor is up-regulated by (a) introducing into the plant aexpression construct comprising a nucleotide sequence selected from thegroup of SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 9, SEQ ID NO: 12 or SEQID NO: 15; and (b) growing the plant under conditions whereby saidexpression construct increases levels of the transcription factor in theplant compared to a control plant grown under similar conditions. In oneembodiment, the alkaloid is a nicotinic alkaloid. In another embodiment,the plant belongs to the genus Nicotiana. In a further embodiment, theplant is Nicotiana tabacum. In another embodiment, the method producesan increased alkaloid plant. In a further embodiment, an increasedalkaloid product is produced from the plant. In a still furtherembodiment, the increased alkaloid is nicotine.

In another aspect, there is provided a method for increasing a nicotinicalkaloid in a plant, comprising down-regulating a transcription factorthat negatively regulates alkaloid biosynthesis and up-regulating atleast one of NBB1, A622, QPT, PMT and MPO. In one embodiment, the plantbelongs to the genus Nicotiana. In a further embodiment, the plant isNicotiana tabacum. In another embodiment, the nicotinic alkaloid isnicotine. In another embodiment, the method produces an increasedalkaloid plant. In a further embodiment, an increased alkaloid productis produced from the plant. In a still further embodiment, the increasedalkaloid is nicotine.

In another aspect, there is provided a method for increasing a nicotinicalkaloid in a plant, comprising up-regulating a transcription factorthat positively regulates alkaloid biosynthesis and up-regulating atleast one of NBB1, A622, QPT, PMT and MPO. In one embodiment, the plantbelongs to the genus Nicotiana. In a further embodiment, the plant isNicotiana tabacum. In another embodiment, the nicotinic alkaloid isnicotine. In another embodiment, the method produces an increasedalkaloid plant. In a further embodiment, an increased alkaloid productis produced from the plant. In a still further embodiment, the increasedalkaloid is nicotine.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts leaf nicotine levels in control and VIGS silenced N.benthamiana plants.

FIG. 2 depicts leaf nicotine levels in N. benthamiana plants transformedwith constructs for overexpression or suppression of NbTF 1.

FIG. 3 depicts leaf nicotine levels in N. benthamiana plants transformedwith constructs for overexpression or suppression of NbTF4.

FIG. 4 depicts leaf nicotine levels in N. benthamiana plants transformedwith constructs for overexpression or suppression of NbTF5.

DETAILED DESCRIPTION OF THE INVENTION

The present inventors have identified six genes encoding transcriptionfactors that regulate the nicotinic alkaloid biosynthetic pathway. Thenucleic acid sequences of the genes have been determined The full-lengthsequence of the NbTFJ gene is set forth in SEQ ID NO: 1. The openreading frame (ORF) of SEQ ID NO: 1, set forth in SEQ ID NO: 2, encodesthe polypeptide sequence set forth in SEQ ID NO: 3. The sequence of aportion of the NbTF3 gene, which includes the fragment used for VIGS, isset forth in SEQ ID NO: 4. The full-length sequence of the NbTF4 gene,including some sequence that is upstream of the transcriptional startsite, is set forth in SEQ ID NO: 5. The ORF of SEQ ID NO: 5, set forthin SEQ ID NO: 6, encodes the polypeptide sequence set forth in SEQ IDNO: 7. The full-length sequence of the NbTF5 gene is set forth in SEQ IDNO: 8. The ORF of SEQ ID NO: 8, set forth in SEQ ID NO: 9, encodes thepolypeptide sequence set forth in SEQ ID NO: 10. The full-lengthsequence of the NbTF6 gene is set forth in SEQ ID NO: 11. The ORF of SEQID NO: 11, set forth in SEQ ID NO: 12, encodes the polypeptide sequenceset forth in SEQ ID NO: 13. The full-length sequence of the NbTF7 geneis set forth in SEQ ID NO: 14. The ORF of SEQ ID NO: 14, set forth inSEQ ID NO: 15, encodes the polypeptide sequence set forth in SEQ ID NO:16.

NbTF1, NbTF4, NbTFS. and NbTF6 positively regulates on alkaloidbiosynthesis. NbTF3 and NbTF7 negatively regulate alkaloid biosynthesis.The transcription factors belong to several different classes oftranscription factors known from plants: NbTF1, NbTF3 and NbTFS are Myc,basic helix-loop-helix transcription factors; NbTF4 is a homeodomainleucine zipper transcription factor; NbTF6 is an AP2, ethylene-responsefactor; and NbTF7 is a B3 domain, auxin response factor.

These transcription factor genes or fragments thereof may be used tosuppress synthesis of alkaloids (e.g., of nicotinic alkaloids) in plantsthat naturally produce the alkaloids. For example, Nicotiana spp. (e.g.N. tabacum, N. rustica and N. benthamiana) naturally produce nicotinicalkaloids. N. tabacum is an agricultural crop of high productivity andbiotechnological uses of this plant continue to increase. Reducingnicotine biosynthesis genetic engineering of transcription factorexpression leads to creating tobacco varieties that contain zero or lownicotine levels for use as low-toxicity production platforms for theproduction of plant-made pharmaceuticals (PMPs) (e.g. recombinantproteins and antibodies) or as industrial, food and biomass crops. Thetranscription factor genes or fragments thereof may be used in plants orplant cells to increase synthesis of alkaloids (e.g., of nicotinicalkaloids) and related compounds, which may have therapeuticapplications.

Definitions

All technical terms employed in this specification are commonly used inbiochemistry, molecular biology and agriculture; hence, they areunderstood by those skilled in the field to which this inventionbelongs. Those technical terms can be found, for example in: MOLECULARCLONING: A LABORATORY MANUAL 3rd ed., vol. 1-3, ed. Sambrook and Russel,Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2001;CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, ed. Ausubel et al., GreenePublishing Associates and Wiley-Interscience, New York, 1988 (includingperiodic updates); SHORT PROTOCOLS IN MOLECULAR BIOLOGY: A COMPENDIUM OFMETHODS FROM CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 5th ed., vol. 1-2,ed. Ausubel et al., John Wiley & Sons, Inc., 2002; GENOME ANALYSIS: ALABORATORY MANUAL, vol. 1-2, ed. Green et al., Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., 1997. Methodology involvingplant biology techniques are described here and also are described indetail in treatises such as METHODS IN PLANT MOLECULAR BIOLOGY: ALABORATORY COURSE MANUAL, ed. Maliga et al., Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., 1995.

By “isolated nucleic acid molecule” is intended a nucleic acid molecule,DNA or RNA, which has been removed from its native environment. Forexample, recombinant DNA molecules contained in a DNA construct areconsidered isolated for the purposes of the present invention. Furtherexamples of isolated DNA molecules include recombinant DNA moleculesmaintained in heterologous host cells or DNA molecules that arepurified, partially or substantially, in solution. Isolated RNAmolecules include in vitro RNA transcripts of the DNA molecules of thepresent invention. Isolated nucleic acid molecules, according to thepresent invention, further include such molecules producedsynthetically.

A “chimeric nucleic acid” comprises a coding sequence or fragmentthereof linked to a nucleotide sequence that is different from thenucleotide sequence with which it is associated in cells in which thecoding sequence occurs naturally.

“Heterologous nucleic acid” refers to a nucleic acid, DNA or RNA, whichhas been introduced into a cell (or the cell's ancestor) which is not acopy of a sequence naturally found in the cell into which it isintroduced. Such heterologous nucleic acid may comprise segments thatare a copy of a sequence which is naturally found in the cell into whichit has been introduced, or fragments thereof.

“Endogenous nucleic acid” or “endogenous sequence” is “native” to, i.e.,indigenous to, the plant or organism that is to be geneticallyengineered. It refers to a nucleic acid, gene, polynucleotide, DNA, RNA,mRNA, or cDNA molecule that is present in the genome of a plant ororganism that is to be genetically engineered.

“Exogenous nucleic acid” refers to a nucleic acid, DNA or RNA, which hasbeen introduced into a cell (or the cell's ancestor) through the effortsof humans. Such exogenous nucleic acid may be a copy of a sequence whichis naturally found in the cell into which it was introduced, orfragments thereof.

The terms “encoding” and “coding” refer to the process by which a gene,through the mechanisms of transcription and translation, providesinformation to a cell from which a series of amino acids can beassembled into a specific amino acid sequence to produce an activeenzyme. Because of the degeneracy of the genetic code, certain basechanges in DNA sequence do not change the amino acid sequence of aprotein.

“Sequence identity” or “identity” in the context of two polynucleotide(nucleic acid) or polypeptide sequences includes reference to theresidues in the two sequences which are the same when aligned formaximum correspondence over a specified region. When percentage ofsequence identity is used in reference to proteins it is recognized thatresidue positions which are not identical often differ by conservativeamino acid substitutions, where amino acid residues are substituted forother amino acid residues with similar chemical properties, such ascharge and hydrophobicity, and therefore do not change the functionalproperties of the molecule. Where sequences differ in conservativesubstitutions, the percent sequence identity may be adjusted upwards tocorrect for the conservative nature of the substitution. Sequences whichdiffer by such conservative substitutions are said to have “sequencesimilarity” or “similarity.” Means for making this adjustment arewell-known to those of skill in the art. Typically this involves scoringa conservative substitution as a partial rather than a full mismatch,thereby increasing the percentage sequence identity. Thus, for example,where an identical amino acid is given a score of 1 and anon-conservative substitution is given a score of zero, a conservativesubstitution is given a score between zero and 1. The scoring ofconservative substitutions is calculated, for example, according to thealgorithm of Meyers & Miller, Computer Applic. Biol. Sci. 4: 11-17(1988), as implemented in the program PC/GENE (Intelligenetics, MountainView, Calif., USA).

Use in this description of a percentage of sequence identity denotes avalue determined by comparing two optimally aligned sequences over acomparison window, wherein the portion of the polynucleotide sequence inthe comparison window may comprise additions or deletions (i.e., gaps)as compared to the reference sequence (which does not comprise additionsor deletions) for optimal alignment of the two sequences. The percentageis calculated by determining the number of positions at which theidentical nucleic acid base or amino acid residue occurs in bothsequences to yield the number of matched positions, dividing the numberof matched positions by the total number of positions in the window ofcomparison, and multiplying the result by 100 to yield the percentage ofsequence identity.

A “variant” is a nucleotide or amino acid sequence that deviates fromthe standard, or given, nucleotide or amino acid sequence of aparticular gene or polypeptide. The terms “isoform,” “isotype,” and“analog” also refer to “variant” forms of a nucleotide or an amino acidsequence. An amino acid sequence that is altered by the addition,removal, or substitution of one or more amino acids, or a change innucleotide sequence, may be considered a variant sequence. A polypeptidevariant may have “conservative” changes, wherein a substituted aminoacid has similar structural or chemical properties, e.g., replacement ofleucine with isoleucine. A polypeptide variant may have“nonconservative” changes, e.g., replacement of a glycine with atryptophan. Analogous minor variations may also include amino aciddeletions or insertions, or both. Guidance in determining which aminoacid residues may be substituted, inserted, or deleted may be foundusing computer programs well known in the art such as Vector NTI Suite(InforMax, MD) software. Variant may also refer to a “shuffled gene”such as those described in Maxygen-assigned patents (e.g. U.S. Pat. No.6,602,986).

“Genetic engineering” encompasses any methodology for introducing anucleic acid or specific mutation into a host organism. For example, aplant is genetically engineered when it is transformed with apolynucleotide sequence that suppresses expression of a gene, such thatexpression of a target gene is reduced compared to a control plant. Aplant is genetically engineered when a polynucleotide sequence isintroduced that results in the expression of a novel gene in the plant,or an increase in the level of a gene product that is naturally found inthe plants. In the present context, “genetically engineered” includestransgenic plants and plant cells, as well as plants and plant cellsproduced by means of targeted mutagenesis effected, for example, throughthe use of chimeric RNA/DNA oligonucleotides, as described by Beetham etal., Proc. Natl. Acad. Sci. U.S.A. 96: 8774-8778 (1999) and Zhu et al.,Proc. Natl. Acad. Sci. U.S,A. 96: 8768-8773 (1999), or so-called“recombinagenic olionucleobases,” as described in International patentpublication WO 2003/013226. Likewise, a genetically engineered plant orplant cell may be produced by the introduction of a modified virus,which, in turn, causes a genetic modification in the host, with resultssimilar to those produced in a transgenic plant, as described herein.See, e.g., U.S. Pat. No. 4,407,956. Additionally, a geneticallyengineered plant or plant cell may be the product of any native approach(i.e., involving no foreign nucleotide sequences), implemented byintroducing only nucleic acid sequences derived from the host plantspecies or from a sexually compatible plant species. See, e.g., U.S.published patent application No. 2004/0107455.

“Promoter” connotes a region of DNA upstream from the start oftranscription that is involved in recognition and binding of RNApolymerase and other proteins to initiate transcription. A “constitutivepromoter” is one that is active throughout the life of the plant andunder most environmental conditions. Tissue-specific, tissue-preferred,cell type-specific, and inducible promoters constitute the class of“non-constitutive promoters.” “Operably linked” refers to a functionallinkage between a promoter and a second sequence, where the promotersequence initiates and mediates transcription of the DNA sequencecorresponding to the second sequence. In general, operably linked meansthat the nucleic acid sequences being linked are contiguous.

As used herein, “expression” denotes the production of an RNA productthrough transcription of a gene or the production of the polypeptideproduct encoded by a nucleotide sequence. “Overexpression” or“up-regulation” is used to indicate that expression of a particular genesequence or variant thereof, in a cell or plant, including all progenyplants derived thereof, has been increased by genetic engineering,relative to a control cell or plant (e.g., “NbTF1 overexpression”).

The terms “suppression” or “down-regulation” are used synonymously toindicate that expression of a particular gene sequence variant thereof,in a cell or plant, including all progeny plants derived thereof, hasbeen reduced by genetic engineering, relative to a control cell or plant(e.g., “NbTF1 down-regulation”).

A “transcription factor” is a protein that binds that binds to DNAregions, typically promoter regions, using DNA binding domains andincreases or decreases the transcription of specific genes. Atranscription factor “positively regulates” alkaloid biosynthesis ifexpression of the transcription factor increases the transcription ofone or more genes encoding alkaloid biosynthesis enzymes and increasesalkaloid production. A transcription factor “negatively regulates”alkaloid biosynthesis if expression of the transcription factordecreases the transcription of one or more genes encoding alkaloidbiosynthesis enzymes and decreases alkaloid production. Transcriptionfactors are classified based on the similarity of their DNA bindingdomains. (see, e.g. Stegmaier et al., Genome Inform. 15 (2): 276-86((2004)). Classes of plant transcription factors include Myc basichelix-loop-helix transcription factors; homeodomain leucine zippertranscription factors; AP2 ethylene-response factor transcriptionfactors; and B3 domain, auxin response factor transcription factors.

An “alkaloid” is a nitrogen-containing basic compound found in plantsand produced by secondary metabolism. A “pyrrolidine alkaloid” is analkaloid containing a pyrrolidine ring as part of its molecularstructure, for example, nicotine. Nicotine and related alkaloids arealso referred to as pyridine alkaloids in the published literature. A“pyridine alkaloid” is an alkaloid containing a pyridine ring as part ofits molecular structure, for example, nicotine. A “nicotinic alkaloid”is nicotine or an alkaloid that is structurally related to nicotine andthat is synthesized from a compound produced in the nicotinebiosynthesis pathway. Illustrative nicotinic alkaloids include but arenot limited to nicotine, nornicotine, anatabine, anabasine, anatalline,N-methylanatabine, N-methylanabasine, myosmine, anabaseine,formylnornicotine, nicotyrine, and cotinine Other very minor nicotinicalkaloids in tobacco leaf are reported, for example, in Hecht et al.,Accounts of Chemical Research 12: 92-98 (1979); Tso, T. G., Production,Physiology and Biochemistry of Tobacco Plant. Ideals Inc., Beltsville,Mo. (1990).

As used herein “alkaloid content” means the total amount of alkaloidsfound in a plant, for example, in terms of pg/g dry weight (DW) or ng/mgfresh weight (FW). “Nicotine content” means the total amount of nicotinefound in a plant, for example, in terms of mg/g DW or FW.

“Plant” is a term that encompasses whole plants, plant organs (e. g.leaves, stems, roots, etc.), seeds, differentiated or undifferentiatedplant cells, and progeny of the same. Plant material includes withoutlimitation seeds, suspension cultures, embryos, meristematic regions,callus tissues, leaves, roots, shoots, stems, fruit, gametophytes,sporophytes, pollen, and microspores.

“Tobacco” or “tobacco plant” refers to any species in the Nicotianagenus that produces nicotinic alkaloids, including but are not limitedto the following: Nicotiana acaulis, Nicotiana acuminata, Nicotianaacuminata var. multzjlora, Nicotiana africana, Nicotiana alata,Nicotiana amplexicaulis, Nicotiana arentsii, Nicotiana attenuata,Nicotiana benavidesii, Nicotiana benthamiana, Nicotiana bigelovii,Nicotiana bonariensis, Nicotiana cavicola, Nicotiana clevelandii,Nicotiana cordifolia, Nicotiana corymbosa, Nicotiana debneyi, Nicotianaexcelsior, Nicotiana forgetiana, Nicotiana fragrans, Nicotiana glauca,Nicotiana glutinosa, Nicotiana goodspeedii, Nicotiana gossei, Nicotianahybrid, Nicotiana ingulba, Nicotiana kawakamii, Nicotiana knightiana,Nicotiana langsdorfi, Nicotiana linearis, Nicotiana longiflora,Nicotiana maritima, Nicotiana megalosiphon, Nicotiana miersii, Nicotiananoctiflora, Nicotiana nudicaulis, Nicotiana obtusifolia, Nicotianaoccidentalis, Nicotiana occidentalis subsp. hesperis, Nicotianaotophora, Nicotiana paniculata, Nicotiana pauczjlora, Nicotianapetunioides, Nicotiana plumbaginifolia, Nicotiana quadrivalvis,Nicotiana raimondii, Nicotiana repanda, Nicotiana rosulata, Nicotianarosulata subsp. ingulba, Nicotiana rotundifolia, Nicotiana rustica,Nicotiana setchellii, Nicotiana simulans, Nicotiana solanifolia,Nicotiana spegauinii, Nicotiana stocktonii, Nicotiana suaveolens,Nicotiana sylvestris, Nicotiana tabacum, Nicotiana thyrsiflora,Nicotiana tomentosa, Nicotiana tomentosifomis, Nicotiana trigonophylla,Nicotiana umbratica, Nicotiana undulata, Nicotiana velutina, Nicotianawigandioides, and interspecific hybrids of the above.

“Tobacco product” refers to a product comprising material produced by aNicotiana plant, including for example, nicotine gum and patches forsmoking cessation, cigarette tobacco including expanded (puffed) andreconstituted tobacco, cigar tobacco, pipe tobacco, cigarettes, cigars,and all forms of smokeless tobacco such as chewing tobacco, snuff, snusand lozenges.

“Decreased alkaloid plant” or “reduced alkaloid plant” encompasses agenetically engineered plant that has a decrease in alkaloid content toa level less than 50%, and preferably less than 10%, 5%, or 1% of thealkaloid content of a control plant of the same species or variety.

“Increased alkaloid plant” encompasses a genetically engineered plantthat has an increase in alkaloid content greater than 10%, andpreferably greater than 50%, 100%, or 200% of the alkaloid content of acontrol plant of the same species or variety.

I. Reducing Alkaloid Production in Plants

A. Decreasing Alkaloids by Suppressing a Transcription Factor thatPositively Regulates Alkaloid Production

Alkaloid (e.g. nicotine) production may be reduced by suppression of anendogenous gene encoding a transcription factor that positivelyregulates alkaloid production using the transcription factor genesequences of the present invention in a number of ways generally knownin the art, for example, RNA interference (RNAi) techniques, artificialmicroRNA techniques, virus-induced gene silencing (VIGS) techniques,antisense techniques, sense co-suppression techniques and targetedmutagenesis techniques. Accordingly, the present invention providesmethodology and constructs for decreasing alkaloid content in a plant,by suppressing a gene encoding a transcription factor that positivelyregulates alkaloid production, such as NbTF 1, NbTF4, NbTF5, and NbTF6.Suppressing more than one gene encoding a transcription factor thatpositively regulates on alkaloid production may further decreasealkaloids levels in a plant.

B. Decreasing Alkaloids by Suppressing a Transcription Factor thatPositively Regulates Alkaloid Production and at Least One AlkaloidBiosynthesis Gene

Previous reports indicate that suppressing an alkaloid biosynthesis genein Nicotiana decreases nicotinic alkaloid content. For example,suppressing QPT reduces nicotine levels. (see U.S. Pat. No. 6,586,661).Suppressing A622 or NBB1 also reduces nicotine levels (see Internationalpatent publication WO 2006/109197), as does suppressing PMT (seeChintapakorn and Hamill. Plant Mol. Biol. 53:87-105 (2003)) or MPO (seeInternational patent publications WO 2008/020333 and 2008/008844; Katohet al., Plant Cell Physiol. 48(3): 550-4 (2007)). Accordingly, thepresent invention contemplates further decreasing nicotinic alkaloidcontent by suppressing one or more of A622, NBB1, QPT, PMT and MPO andsuppressing a transcription factor that positively regulates alkaloidproduction. Pursuant to this aspect of the invention, a nucleic acidconstruct comprising at least a fragment of one or more of NbTF1, NbTF4,NbTF5, and NbTF6 and at least a fragment one or more of A622, NBB1, QPT,PMT, and MPO are introduced into a cell or plant. An illustrativenucleic acid construct may comprise both a fragment of NbTF1 and QPT.

C. Decreasing Alkaloids by Overexpressing a Transcription Factor with aNegative Regulatory Effect on Alkaloid Production

Alkaloid (e.g. nicotine) production may be reduced by overexpression ofa gene encoding a transcription factor that negatively regulatesalkaloid production using the transcription factor gene sequences of thepresent invention in a number of ways generally known in the art.Accordingly, the present invention provides methodology and constructsfor decreasing alkaloid content in a plant, by overexpressing a geneencoding a transcription factor that negatively regulates alkaloidproduction, such as NbTF3 or NbTF7. Overexpressing more than one geneencoding a transcription factor that negatively regulates alkaloidproduction may further decrease alkaloids levels in a plant.

D. Decreasing Alkaloids by Overexpressing a Transcription Factor thatNegatively Regulates Alkaloid Production and Suppression at Least OneAlkaloid Biosynthesis Gene

As described in (I)(B) above, it is known that nicotinic alkaloidcontent can be decreased by suppressing an alkaloid biosynthesis gene.Accordingly, the present invention contemplates further decreasingnicotinic alkaloid content by suppressing one or more of A622, NBB1,QPT, PMT and MPO and overexpressing a transcription factor with anegative regulatory effect on alkaloid production. Pursuant to thisaspect of the invention, a nucleic acid construct comprising one or moreof NbTF3 or NbTF7 or their ORFs and at least a fragment of one or moreof A622, NBB1, QPT, PMT, and MPO are introduced into a cell or plant. Anillustrative nucleic acid construct may comprise both the NbTF3 ORF andat least a fragment of QPT.

E. Decreasing Alkaloids by Suppressing a Transcription Factor thatNegatively Regulates Alkaloid Production and Overexpressing aTranscription Factor that Positively Regulates Alkaloid Production

The present invention further contemplates decreasing nicotinic alkaloidcontent by suppressing one or more of NbTF1, NbTF4, NbTF5, and NbTF6 andoverexpressing one or more of NbTF3 or NbTF7.

II. Increasing Alkaloid Production

A. Increasing Alkaloids by Overexpressing a Transcription Factor thatPositively Regulates Alkaloid Production

The present invention also relates to increasing alkaloids in plants byoverexpressing a transcription factor with a positive regulatory effecton alkaloid production. One or more of the NbTF1, NbTF4,NbTF5, and NbTF6genes or their open reading frames may be used to engineeroverproduction of alkaloids, for example nicotinic alkaloids (e.g.nicotine) in plants or plant cells.

B. Increasing Alkaloids by Overexpressing a Transcription Factor thatPositively Regulates Alkaloid Production and at Least One at Least OneAlkaloid Biosynthesis Gene

Alkaloids, such as nicotine, can be increased by overexpressing one ormore genes encoding enzymes in the alkaloid biosynthesis pathway. Seefor example Sato et al. Proc. Natl. Acad. Sci. U.S.A. 98(1):367-72(2001). The effect of overexpressing PMT alone on nicotine content ofleaves was an increase of only 40% despite 4- to 8-fold increases in PMTtranscript levels in roots, suggesting that limitations at other stepsof the pathway prevented a larger effect. Therefore, the presentinvention contemplates that overexpressing a transcription factor with apositive regulatory effect on alkaloid production and at least one atleast one alkaloid biosynthesis gene, such as PMT, will result ingreater alkaloid production than up-regulating the alkaloid biosynthesisgene alone.

Pursuant to this aspect of the invention, a nucleic acid constructcomprising one or more of NbTF1, NbTF4, NbTF5, and NbTF6 genes or theiropen reading frames and at least one of A622, NBBJ, QPT, PMT, and MPO isintroduced into a plant cell. An illustrative nucleic acid construct maycomprise, for example, both NbTFJ and PMT. Similarly, for example, agenetically engineered plant overexpressing NbTFJ and PMT may beproduced by crossing a transgenic plant overexpressing NbTFJ1 with atransgenic plant overexpressing PMT. Following successive rounds ofcrossing and selection, a genetically engineered plant overexpressingNbTFJ1 and PMT can be selected.

C. Increasing Alkaloids by Suppressing a Transcription Factor thatNegatively Regulates Alkaloid Production

Alkaloid (e.g. nicotine) production may be increased by suppression of agene encoding a transcription factor that negatively regulates alkaloidproduction using the transcription factor gene sequences of the presentinvention in a number of ways generally known in the art. Accordingly,the present invention provides methodology and constructs for increasingalkaloid content in a plant, by suppressing a gene encoding atranscription factor that negatively regulates alkaloid production, suchas NbTF3 or NbTF7. Suppressing more than one gene encoding atranscription factor that negatively regulates alkaloid production mayfurther increase alkaloids levels in a plant.

D. Increasing Alkaloids by Suppressing a Transcription Factor thatNegatively Regulates Alkaloid Production And Overexpressing at Least OneAlkaloid Biosynthesis Gene

As described in (II)(B) above, it is known that nicotinic alkaloidcontent can be increased by overexpressing an alkaloid biosynthesisgene. Accordingly, the present invention contemplates further increasingnicotinic alkaloid content by overexpressing one or more of A622, NBB1,QPT, PMT and MPO and suppressing a transcription factor with a negativeregulatory effect on alkaloid production. Pursuant to this aspect of theinvention, a nucleic acid construct comprising at least a fragment ofNbTF3 or NbTF7 and one or more of A622, NBB1, QPT, PMT, and MPO areintroduced into a cell or plant. An illustrative nucleic acid constructmay comprise both a fragment of NbTF3 and QPT.

E. Increasing Alkaloids by Overexpressing a Transcription Factor thatPositively Regulates Alkaloid Production and Suppressing a TranscriptionFactor that Negatively Regulates Alkaloid Production

The present invention further contemplates increasing nicotinic alkaloidcontent by overexpressing one or more of NbTF 1, NbTF4, NbTF5, and NbTF6and suppressing one or more of NbTF3 or NbTF7.

III. Altering Content of Minor Alkaloids, Alkaloid Precursors, andRelated Compounds

It is known that suppression of an alkaloid biosynthesis gene canincrease the accumulation of precursor compounds or increase therelative content of minor alkaloids. For example, suppression of PMT inN. tabacum resulted in an increase in anatabine. (Chintapakorn andHamill. Plant Mol. Biol. 53:87-105 (2003)) Suppression of a cytochromeP450 (littorine hydroxylase/mutase) involved in tropane alkaloidbiosynthesis in Hyoscyamus niger resulted in accumulation of theintermediate littorine, which immediately precedes the blocked step (Liet al., Chem. Biol. 13:513-20 (2006)). Up-regulation of the alkaloidpathway by overexpression of a transcription factor that positivelyregulates alkaloid production or suppression of a transcription factorthat negatively regulates alkaloid production, while also suppressing analkaloid biosynthesis gene can result in a further increase in minoralkaloid, alkaloid precursor, or related compound. Pursuant to thisaspect of the invention, a nucleic acid construct comprising one or moreof NbTF1, NbTF4, NbTF5, and NbTF6 or their open reading frames and atleast a fragment of one of A622, NBB1, QPT, PMT, and MPO is introducedinto a plant cell. Alternatively, a nucleic acid construct comprising atleast a fragment of NbTF3 or NbTF7 and at least a fragment of one ormore of A622, NBB1, QPT, PMT, and MPO are introduced into a cell orplant. An illustrative nucleic acid construct may comprise both afragment of NbTF3 and a fragment of PMT.

IV. Genetic Engineering of Plants and Cells Using Transcription FactorSequences that Regulate Alkaloid Production

Transcription Factor Sequences

Transcription factor genes have been identified in several plantspecies, exemplified by Nicotiana plants. Accordingly, the presentinvention embraces any nucleic acid, gene, polynucleotide, DNA, RNA,mRNA, or cDNA molecule that is isolated from the genome of a plantspecies, or produced synthetically, that encodes a transcription factorthat regulates alkaloid biosynthesis. The DNA or RNA may bedouble-stranded or single-stranded. Single-stranded DNA may be thecoding strand, also known as the sense strand, or it may be thenon-coding strand, also called the anti-sense strand.

It is understood to one skilled in the art that transcription factorgenes of the present invention include the sequences set forth in SEQ IDNO: 1, SEQ ID NO: 4, SEQ ID NO:5, SEQ ID NO: 8, SEQ ID NO: 11, SEQ IDNO: 14 and SEQ ID NO: 15, including fragments thereof at least about 21consecutive nucleotides, which are of a sufficient length as to beuseful in induction of gene silencing in plants (Hamilton and Baulcombe,Science 286, 950-952 (1999)).

The invention includes as well as nucleic acid molecules comprised of“variants” of SEQ ID NO: 1, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 8,SEQ ID NO: 11, SEQ ID NO: 14, and SEQ ID NO: 15, with one or more basesdeleted, substituted, inserted, or added, which variant codes for apolypeptide that regulates alkaloid biosynthesis activity. Accordingly,sequences having “base sequences with one or more bases deleted,substituted, inserted, or added” retain physiological activity even whenthe encoded amino acid sequence has one or more amino acids substituted,deleted, inserted, or added. Additionally, multiple forms oftranscription factors NbTF1, NbTF3, NbTF4, NbTF5, NbTF6 and NbTF7 mayexist, which may be due to post-translational modification of a geneproduct, or to multiple forms of the transcription factor gene.Nucleotide sequences that have such modifications and that code for atranscription factor that regulates alkaloid biosynthesis are includedwithin the scope of the present invention.

For example, the poly A tail or 5′-or 3′-end, nontranslated regions maybe deleted, and bases may be deleted to the extent that amino acids aredeleted. Bases may also be substituted, as long as no frame shiftresults. Bases also may be “added” to the extent that amino acids areadded. It is essential, however, that any such modification does notresult in the loss of transcription factor activity that regulatesalkaloid biosynthesis. A modified DNA in this context can be obtained bymodifying the DNA base sequences of the invention so that amino acids atspecific sites in the encoded polypeptide are substituted, deleted,inserted, or added by site-specific mutagenesis, for example. (seeZoller & Smith, Nucleic Acid Res. 10: 6487-500 (1982)).

A transcription factor sequence can be synthesized ab initio from theappropriate bases, for example, by using an appropriate protein sequencedisclosed herein as a guide to create a DNA molecule that, thoughdifferent from the native DNA sequence, results in the production of aprotein with the same or similar amino acid sequence.

Unless otherwise indicated, all nucleotide sequences determined bysequencing a DNA molecule herein were determined using an automated DNAsequencer, such as the Model 3730x1 from Applied Biosystems, Inc.Therefore, as is known in the art for any DNA sequence determined bythis automated approach, any nucleotide sequence determined herein maycontain some errors. Nucleotide sequences determined by automation aretypically at least about 95% identical, more typically at least about96% to at least about 99.9% identical to the actual nucleotide sequenceof the sequenced DNA molecule. The actual sequence can be more preciselydetermined by other approaches including manual DNA sequencing methodswell known in the art. As is also known in the art, a single insertionor deletion in a determined nucleotide sequence compared to the actualsequence will cause a frame shift in translation of the nucleotidesequence such that the predicted amino acid sequence encoded by adetermined nucleotide sequence may be completely different from theamino acid sequence actually encoded by the sequenced DNA molecule,beginning at the point of such an insertion or deletion.

For the purpose of the invention, two sequences hybridize understringent conditions when they form a double-stranded complex in ahybridization solution of 6× SSE, 0.5% SDS, 5× Denhardt's solution and100 μg of non-specific carrier DNA. See Ausubel et al., supra, atsection 2.9, supplement 27 (1994). Sequences may hybridize at “moderatestringency,” which is defined as a temperature of 60° C. in ahybridization solution of 6× SSE, 0.5% SDS, 5× Denhardt's solution and100 μg of non-specific carrier DNA. For “high stringency” hybridization,the temperature is increased to 68° C. Following the moderate stringencyhybridization reaction, the nucleotides are washed in a solution of 2×SSE plus 0.05% SDS for five times at room temperature, with subsequentwashes with 0.1× SSC plus 0.1% SOS at 60° C. for 1 h. For highstringency, the wash temperature is increased to 68° C. For the purposeof the invention, hybridized nucleotides are those that are detectedusing 1 ng of a radiolabeled probe having a specific radioactivity of10,000 cpm/ng, where the hybridized nucleotides are clearly visiblefollowing exposure to X-ray film at −70° C. for no more than 72 hours.

The present application is directed to such nucleic acid molecules whichare at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%or 100% identical to a nucleic acid sequence described in any of SEQ IDNO: 1-2. Preferred are nucleic acid molecules which are at least 95%,96%, 97%, 98%, 99% or 100% identical to the nucleic acid sequence shownin any of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 5, SEQ IDNO:6, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 12, SEQ IDNO: 14, and SEQ ID NO: 15. Differences between two nucleic acidsequences may occur at the 5′ or 3′ terminal positions of the referencenucleotide sequence or anywhere between those terminal positions,interspersed either individually among nucleotides in the referencesequence or in one or more contiguous groups within the referencesequence.

As a practical matter, whether any particular nucleic acid molecule isat least 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a referencenucleotide sequence refers to a comparison made between two moleculesusing standard algorithms well known in the art and can be determinedconventionally using publicly available computer programs such as theBLASTN algorithm. See Altschul et al., Nucleic Acids Res. 25: 3389-402(1997).

The present invention further provides nucleic acid molecules comprisingthe nucleotide sequence of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 4, SEQID NO: 5, SEQ ID NO:6, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ IDNO: 12, SEQ ID NO: 14, and SEQ ID NO: 15, which encode a transcriptionfactor polypeptide, wherein the polypeptide has an amino acid sequencethat corresponds to SEQ ID NO: 3, SEQ ID NO: 7, SEQ ID NO: 10, SEQ IDNO: 13, or SEQ ID NO: 16, and wherein the polypeptide of the inventionencompasses amino acid substitutions, additions and deletions that donot alter the function of the transcription factor polypeptide.

Methodology for Suppressing a Transcription Factor that RegulatesAlkaloid Production

In one aspect of the invention, methods and constructs are provided forsuppressing a transcription factor that regulates alkaloid production,altering alkaloid levels, and producing plants with altered alkaloidlevels. While any method may be used for suppressing a transcriptionfactor that regulates alkaloid production, the present inventioncontemplates antisense, sense co-suppression, RNAi, artificial microRNA,virus-induced gene silencing (VIGS), antisense, sense co-suppression,and targeted mutagenesis approaches.

RNAi techniques involve stable transformation using RNAi plasmidconstructs (Helliwell and Waterhouse, Methods Enzymol. 392:24-35(2005)). Such plasmids are composed of a fragment of the target gene tobe silenced in an inverted repeat structure. The inverted repeats areseparated by a spacer, often an intron. The RNAi construct driven by asuitable promoter, for example, the Cauliflower mosaic virus (CaMV) 35Spromoter, is integrated into the plant genome and subsequenttranscription of the transgene leads to an RNA molecule that folds backon itself to form a double-stranded hairpin RNA. This double-strandedRNA structure is recognized by the plant and cut into small RNAs (about21 nucleotides long) called small interfering RNAs (siRNAs). siRNAsassociate with a protein complex (RISC) which goes on to directdegradation of the mRNA for the target gene.

Artificial microRNA (amiRNA) techniques exploit the microRNA (miRNA)pathway that functions to silence endogenous genes in plants and othereukaryotes (Schwab et al., Plant Cell 18:1121-33 (2006); Alvarez et al,Plant Cell 18:1134-51 (2006)). In this method, 21 nucleotide longfragments of the gene to be silenced are introduced into a pre-miRNAgene to form a pre-amiRNA construct. The pre-miRNA construct istransferred into the plant genome using transformation methods apparentto one skilled in the art. After transcription of the pre-amiRNA,processing yields amiRNAs that target genes, which share nucleotideidentity with the 21 nucleotide amiRNA sequence.

In RNAi silencing techniques, two factors can influence the choice oflength of the fragment. The shorter the fragment the less frequentlyeffective silencing will be achieved, but very long hairpins increasethe chance of recombination in bacterial host strains. The effectivenessof silencing also appears to be gene dependent and could reflectaccessibility of target mRNA or the relative abundances of the targetmRNA and the hpRNA in cells in which the gene is active. A fragmentlength of between 100 and 800 bp, preferably between 300 and 600 bp, isgenerally suitable to maximize the efficiency of silencing obtained. Theother consideration is the part of the gene to be targeted. 5′ UTR,coding region, and 3′ UTR fragments can be used with equally goodresults. As the mechanism of silencing depends on sequence homologythere is potential for cross-silencing of related mRNA sequences. Wherethis is not desirable a region with low sequence similarity to othersequences, such as a 5′ or 3′ UTR, should be chosen. The rule foravoiding cross-homology silencing appears to be to use sequences that donot have blocks of sequence identity of over 20 bases between theconstruct and the non-target gene sequences. Many of these sameprinciples apply to selection of target regions for designing amiRNAs.

Virus-induced gene silencing (VIGS) techniques are a variation of RNAitechniques that exploits the endogenous-antiviral defenses of plants.Infection of plants with recombinant VIGS viruses containing fragmentsof host DNA leads to post-transcriptional gene silencing for the targetgene. In one embodiment, a tobacco rattle virus (TRV) based VIGS systemcan be used. Tobacco rattle virus based VIGS systems are described forexample, in Baulcombe, Curr. Opin. Plant Biol. 2: 109-113 (1999); Lu, etal., Methods 30: 296-303 (2003); Ratcliff, et al., The Plant Journal 25:237-245 (2001); and U.S. Pat. No. 7,229,829.

Antisense techniques involve introducing into a plant an antisenseoligonucleotide that will bind to the messenger RNA (mRNA) produced bythe gene of interest. The “antisense” oligonucleotide has a basesequence complementary to the gene's messenger RNA (mRNA), which iscalled the “sense” sequence. Activity of the sense segment of the mRNAis blocked by the anti-sense mRNA segment, thereby effectivelyinactivating gene expression. Application of antisense to gene silencingin plants is described in more detail in Stam et al., Plant J. 21 :27-42(2000).

Sense co-suppression techniques involve introducing a highly expressedsense transgene into a plant resulting in reduced expression of both thetransgene and the endogenous gene (Depicker and van Montagu, Curr. Opin.Cell Biol. 9: 373-82 (1997)). The effect depends on sequence identitybetween transgene and endogenous gene.

Targeted mutagenesis techniques, for example TILLING (Targeting InducedLocal Lesions IN Genomes) and “delete-a-gene” using fast-neutronbombardment, may be used to knockout gene function in a plant (Henikoff,et al., Plant Physiol. 135: 630-6 (2004); Li et al., Plant J. 27:235-242 (2001)). TILLING involves treating seeds or individual cellswith a mutagen to cause point mutations that are then discovered ingenes of interest using a sensitive method for single-nucleotidemutation detection. Detection of desired mutations (e.g. mutationsresulting in the inactivation of the gene product of interest) may beaccomplished, for example, by PCR methods. For example, oligonucleotideprimers derived from the gene of interest may be prepared and PCR may beused to amplify regions of the gene of interest from plants in themutagenized population. Amplified mutant genes may be annealed towild-type genes to find mismatches between the mutant genes andwild-type genes. Detected differences may be traced back to the plantswhich had the mutant gene thereby revealing which mutagenized plantswill have the desired expression (e.g. silencing of the gene ofinterest). These plants may then be selectively bred to produce apopulation having the desired expression. TILLING can provide an allelicseries that includes missense and knockout mutations, which exhibitreduced expression of the targeted gene. TILLING is touted as a possibleapproach to gene knockout that does not involve introduction oftransgenes, and therefore may be more acceptable to consumers.Fast-neutron bombardment induces mutations, i.e. deletions, in plantgenomes that can also be detected using PCR in a manner similar toTILLING.

Nucleic Acid Constructs

In accordance with one aspect of the invention, a sequence thatsuppresses a transcription factor that regulates alkaloid biosynthesisis incorporated into a nucleic acid construct that is suitable forintroducing into a plant or cell. Thus, such a nucleic acid constructcan be used to suppress at least one of NbTF1, NbTF3 NbTF4, NbTF5, NbTF6and NbTF7. and optionally at least one of A622, NBB1, PMT, QPT, and MPOin a plant or cell.

In another aspect of the invention, a sequence that increases activityof transcription factor that regulates alkaloid biosynthesis isincorporated into a nucleic acid construct that is suitable forintroducing into a plant or cell. Thus, such a nucleic acid constructcan be used to overexpress NbTF1, NbTF3, NbTF4, NbTF5, NbTF6 and NbTF7,and optionally at least one of A622, NBB1, PMT, and QPT, and MPO in aplant or cell.

Recombinant nucleic acid constructs may be made using standardtechniques. For example, the DNA sequence for transcription may beobtained by treating a vector containing said sequence with restrictionenzymes to cut out the appropriate segment. The DNA sequence fortranscription may also be generated by annealing and ligating syntheticoligonucleotides or by using synthetic oligonucleotides in a polymerasechain reaction (PCR) to give suitable restriction sites at each end. TheDNA sequence then is cloned into a vector containing suitable regulatoryelements, such as upstream promoter and downstream terminator sequences.

An important aspect of the present invention is the use of nucleic acidconstructs wherein an a sequence encoding a transcription factor thatregulates alkaloid biosynthesis is operably linked to one or moreregulatory sequences, which drive expression of the transcriptionfactor-encoding sequence in certain cell types, organs, or tissueswithout unduly affecting normal development or physiology.

Promoters useful for expression of a nucleic acid sequence introducedinto a cell to either decrease or increase expression of a transcriptionfactor that regulates alkaloid biosynthesis may be constitutivepromoters, such as the carnation etched ring virus (CERV), cauliflowermosaic virus (CaMV) 35S promoter, or more particularly the doubleenhanced cauliflower mosaic virus promoter, comprising two CaMV 35Spromoters in tandem (referred to as a “Double 35S” promoter).Tissue-specific, tissue-preferred, cell type-specific, and induciblepromoters may be desirable under certain circumstances. For example, atissue-specific promoter allows for overexpression in certain tissueswithout affecting expression in other tissues.

Preferred promoters include promoters which are active in root tissues,such as the tobacco RB7promoter (Hsu et al., Pestic. Sci. 44: 9-19(1995); U.S. Pat. No. 5,459,252), maize promoter CRWAQ81 (U.S. publishedpatent application 20050097633); the Arabidopsis ARSK1 promoter (Hwangand Goodman, Plant J. 8:37-43 (1995)), the maize MR7 promoter (U.S. Pat.No. 5,837,848), the maize ZRP2 promoter (U.S. Pat. No. 5,633,363), themaize MTL promoter (U.S. Pat. Nos. 5,466,785 and 6,018,099) the maizeMRS1, MRS2, MRS3, and MRS4 promoters (U.S. Patent Publication No.20050010974), an Arabidopsis cryptic promoter (U.S. Patent PublicationNo. 20030106105) and promoters that are activated under conditions thatresult in elevated expression of enzymes involved in nicotinebiosynthesis such as the tobacco RD2 promoter (U.S. Pat. No. 5,837,876),PMT promoters (Shoji et al., Plant Cell Physiol. 41: 831-39 (2000); WO2002/038588) or an A622 promoter (Shoji, et al., Plant Mol. Biol. 50:427-40 (2002)).

The vectors of the invention may also contain termination sequences,which are positioned downstream of the nucleic acid molecules of theinvention, such that transcription of mRNA is terminated, and polyAsequences added. Exemplary of such terminators include Agrobacteriumtumefaciens nopaline synthase terminator (Tnos), Agrobacteriumtumefaciens mannopine synthase terminator (Tmas) and the CaMV 35Sterminator (T35S). Particularly preferred termination regions for useaccording to the invention include the pea ribulose bisphosphatecarboxylase small subunit termination region (TrbcS) or the Tnostermination region. The expression vector also may contain enhancers,start codons, splicing signal sequences, and targeting sequences.

Expression vectors of the invention may also contain a selection markerby which transformed cells can be identified in culture. The marker maybe associated with the heterologous nucleic acid molecule, i.e., thegene operably linked to a promoter. As used herein, the term “marker”refers to a gene encoding a trait or a phenotype that permits theselection of, or the screening for, a plant or cell containing themarker. In plants, for example, the marker gene will encode antibioticor herbicide resistance. This allows for selection of transformed cellsfrom among cells that are not transformed or transfected.

Examples of suitable selectable markers include adenosine deaminase,dihydrofolate reductase, hygromycin-B-phosphotransferase, thymidinekinase, xanthine-guanine phospho-ribosyltransferase, glyphosate andglufosinate resistance, and amino-glycoside 3′-O-phosphotransferase(kanamycin, neomycin and G418 resistance). These markers may includeresistance to G418, hygromycin, bleomycin, kanamycin, and gentamicin.The construct may also contain the selectable marker gene bar thatconfers resistance to herbicidal phosphinothricin analogs like ammoniumgluphosinate. Thompson et al, EMBO J. 9: 2519-23 (1987). Other suitableselection markers are known as well.

Visible markers such as green florescent protein (GFP) may be used.Methods for identifying or selecting transformed plants based on thecontrol of cell division have also been described. See WO 2000/052168and WO 2001/059086.

Replication sequences, of bacterial or viral origin, may also beincluded to allow the vector to be cloned in a bacterial or phage host.Preferably, a broad host range prokaryotic origin of replication isused. A selectable marker for bacteria may be included to allowselection of bacterial cells bearing the desired construct. Suitableprokaryotic selectable markers also include resistance to antibioticssuch as kanamycin or tetracycline.

Other nucleic acid sequences encoding additional functions may also bepresent in the vector, as is known in the art. For instance, whenAgrobacterium is the host, T-DNA sequences may be included to facilitatethe subsequent transfer to and incorporation into plant chromosomes.

Such gene constructs may suitably be screened for activity bytransformation into a host plant via Agrobacterium and screening formodified alkaloid levels.

Suitably, the nucleotide sequences for the genes may be extracted fromthe Genbank™ nucleotide database and searched for restriction enzymesthat do not cut. These restriction sites may be added to the genes byconventional methods such as incorporating these sites in PCR primers orby sub-cloning.

Preferably, constructs are comprised within a vector, most suitably anexpression vector adapted for expression in an appropriate host (plant)cell. It will be appreciated that any vector which is capable ofproducing a plant comprising the introduced DNA sequence will besufficient.

Suitable vectors are well known to those skilled in the art and aredescribed in general technical references such as Pouwels et al, CloningVectors. A Laboratory Manual, Elsevier, Amsterdam (1986). Particularlysuitable vectors include the Ti plasmid vectors.

Host Plants and Cells

The present invention comprehends the genetic manipulation of a plant orcell via introducing a polynucleotide sequence that encodes atranscription factor that regulates alkaloid biosynthesis. Accordingly,the present invention provides methodology and constructs for reducingor increasing alkaloid synthesis in a plant. Additionally, the inventionprovides methods for producing alkaloids and related compounds in aplant cell.

A. Plants

The class of plants which can be used in the present invention isgenerally as broad as the class of alkaloid-producing higher plantsamenable to genetic engineering techniques, including bothmonocotyledonous and dicotyledonous plants, as well as gymnosperms. Apreferred alkaloid-producing plant includes a nicotinicalkaloid-producing plant of the Nicotiana, Duboisia, Solanum,Anthocercis, and Salpiglessis genera in the Solanaceae or the Ecliptaand Zinnia genera in the Compositae.

As known in the art, there are a number of ways by which genes and geneconstructs can be introduced into plants, and a combination of planttransformation and tissue culture techniques have been successfullyintegrated into effective strategies for creating transgenic cropplants.

These methods, which can be used in the present invention, have beendescribed elsewhere (Potrykus, Annu. Rev. Plant Physiol. Plant Mol.Biol. 42: 205-225 (1991); Vasil, Plant Mol. Biol. 5: 925-937 (1994);Walden and Wingender, Trends Biotechnol. 13: 324-331 (1995); Songstad,et al., Plant Cell, Tissue and Organ Culture 40: 1-15 (1995)), and arewell known to persons skilled in the art. For example, one skilled inthe art will certainly be aware that, in addition toAgrobacterium-mediated transformation of Arabidopsis by vacuuminfiltration (Bechtold et al., C.R. Acad. Sci. Ser. III Sci. Vie, 316:1194-1199 (1993)) or wound inoculation (Katavic et al., Mol. Gen. Genet.245: 363-370 (1994)), it is equally possible to transform other plantand crop species, using Agrobacterium Ti-plasmid-mediated transformation(e.g., hypocotyl (DeBlock et al., Plant Physiol. 91: 694-701 (1989)) orcotyledonary petiole (Moloney et al., Plant Cell Rep. 8: 238-242 (1989)wound infection), particle bombardment/biolistic methods (Sanford etal., J. Part. Sci. Technol. 5: 27-37 (1987); Nehra et al., Plant J. 5:285-297 (1994); Becker et al., Plant J. 5: 299-307 (1994)) orpolyethylene glycol-assisted protoplast transformation (Rhodes et al.,Science 240: 204-207 (1988); Shimamoto et al., Nature 335: 274-276(1989)) methods.

Agrobacterium rhizogenes may be used to produce transgenic hairy rootscultures of plants, including tobacco, as described, for example, byGuillon et al., Curr. Opin. Plant Biol. 9: 341-6 (2006). “Tobacco hairyroots” refers to tobacco roots that have T-DNA from an Ri plasmid ofAgrobacterium rhizogenes integrated in the genome and grow in culturewithout supplementation of auxin and other phytohormones. Tobacco hairyroots produce nicotinic alkaloids as roots of a whole tobacco plant do.

Additionally, plants may be transformed by Rhizobium, Sinorhizobium orMesorhizobium transformation. (Broothaerts et al., Nature 433: 629-633(2005)).

After transformation of the plant cells or plant, those plant cells orplants into which the desired DNA has been incorporated may be selectedby such methods as antibiotic resistance, herbicide resistance,tolerance to amino-acid analogues or using phenotypic markers.

Various assays may be used to determine whether the plant cell shows achange in gene expression, for example, Northern blotting orquantitative reverse transcriptase PCR (RT-PCR). Whole transgenic plantsmay be regenerated from the transformed cell by conventional methods.Such transgenic plants may be propagated and self pollinated to producehomozygous lines. Such plants produce seeds containing the genes for theintroduced trait and can be grown to produce plants that will producethe selected phenotype.

Modified alkaloid content, effected in accordance with the presentinvention, can be combined with other traits of interest, such asdisease resistance, pest resistance, high yield or other traits. Forexample, a stable genetically engineered transformant that contains asuitable transgene that modifies alkaloid content may be employed tointrogress a modified alkaloid content trait into a desirablecommercially acceptable genetic background, thereby obtaining a cultivaror variety that combines a modified alkaloid level with said desirablebackground. For example, a genetically engineered tobacco plant withreduced nicotine may be employed to introgress the reduced nicotinetrait into a tobacco cultivar with disease resistance trait, such asresistance to TMV, blank shank, or blue mold. Alternatively, cells of amodified alkaloid content plant of the present invention may betransformed with nucleic acid constructs conferring other traits ofinterest.

B. Cells

The invention contemplates genetically engineering a cell with a nucleicacid sequence encoding a transcription factor that regulates alkaloidbiosynthesis. Illustrative cells include but are not limited to cells ofplants such Nicotiana tabacum, Atropa belladonna, Hyoscyamus niger.

Additionally, cells expressing alkaloid biosynthesis genes may besupplied with precursors to increase substrate availability for alkaloidsynthesis. Cells may be supplied with analogs of precursors which may beincorporated into analogs of naturally occurring alkaloids.

Constructs according to the invention may be introduced into any plantcell, using a suitable technique, such as Agrobacterium-mediatedtransformation, particle bombardment, electroporation, and polyethyleneglycol fusion, or cationic lipid-mediated transfection.

Such cells may be genetically engineered with a nucleic acid constructof the present invention without the use of a selectable or visiblemarker and transgenic organisms may be identified by detecting thepresence of the introduced construct. The presence of a protein,polypeptide, or nucleic acid molecule in a particular cell can bemeasured to determine if, for example, a cell has been successfullytransformed or transfected. For example, and as routine in the art, thepresence of the introduced construct can be detected by PCR or othersuitable methods for detecting a specific nucleic acid or polypeptidesequence. Additionally, genetically engineered cells may be identifiedby recognizing differences in the growth rate or a morphological featureof a transformed cell compared to the growth rate or a morphologicalfeature of a non-transformed cell that is cultured under similarconditions. See WO 2004/076625.

IV. Quantifying Alkaloid Content A. Reduced Alkaloids

Pursuant to one aspect of the invention, genetically engineered plantsand cells are characterized by reduced alkaloid content.

A quantitative reduction in alkaloid levels can be assayed by severalmethods, as for example by quantification based on gas-liquidchromatography, high performance liquid chromatography,radio-immunoassays, and enzyme-linked immunosorbent assays. In thepresent invention, alkaloid levels were measured by HPLC analysisperformed on a Waters 2695 separations module equipped with a WatersX-Terra RP18 5 μm 4.6×150 mm with precolumn at a column temperature of60°. The isocratic elution system consisted of 80% A:20% B where solventA consisted of 50 mM citrate, 10 mM octanesulfonic acid pH 3.0 (adjustedwith triethylamine) containing 5% methanol and solvent B was methanolover 15 min at a flow rate of 1 ml/min. Injection volume was 20 μl.Nicotine was detected at 261 nm via photodiode array detection.

In describing a plant of the invention, the phrase “decreased alkaloidplant” or “reduced alkaloid plant” encompasses a plant that has adecrease in alkaloid content to a level less than 50%, and preferablyless than 10%, 5%, or 1% of the alkaloid content of a control plant ofthe same species or variety.

B. Increased Alkaloids

In one aspect of the invention, genetically engineered plants arecharacterized by increased alkaloid content. Similarly, geneticallyengineered cells are characterized by increased alkaloid production.

In describing a plant of the invention, the phrase “increased alkaloidplant” encompasses a genetically engineered plant that has an increasein alkaloid content greater than 10%, and preferably greater than 50%,100%, or 200% of the alkaloid content of a control plant of the samespecies or variety.

A successfully genetically engineered cell is characterized by increasedalkaloid synthesis. For example, an inventive genetically engineeredcell may produce more nicotine compared to a control cell.

A quantitative increase in nicotinic alkaloid levels can be assayed byseveral methods, as for example by quantification based on gas-liquidchromatography, high performance liquid chromatography,radio-immunoassays, and enzyme-linked immunosorbent assays. In thepresent invention, alkaloid levels were measured by high performanceliquid chromatography with a reversed phase column and a photodiodearray detector as described above.

Products

The polynucleotide sequences that encode transcription factors thatregulate alkaloid biosynthesis may be used for production of plants withaltered alkaloid levels. Such plants may have useful properties, such asincreased pest resistance in the case of increased-alkaloid plants, orreduced toxicity and increased palatability in the case ofdecreased-alkaloid plants.

Plants of the present invention may be useful in the production ofproducts derived from harvested portions of the plants. For example,decreased-alkaloid tobacco plants may be useful in the production ofreduced-nicotine cigarettes for smoking cessation. Increased-alkaloidtobacco plants may be useful in the production of modified risk tobaccoproducts.

Additionally, plants and cells of the present invention may be useful inthe production of alkaloids or alkaloid analogs including nicotineanalogs, which may be used as therapeutics, insecticides, or syntheticintermediates. To this end, large-scale or commercial quantities ofalkaloids and related compounds can be produced by a variety of methods,including extracting compounds from genetically engineered plant, cell,or culture system, including but not limited to hairy root cultures,suspension cultures, callus cultures, and shoot cultures.

In the following examples, functional genomics was used to elucidate sixgenes, NbTF1, NbTF2, NbTF4, NbTF5, NbTF6 and NbTF7, that encodetranscription factors, that regulate alkaloid accumulation in Nicotianabenthamiana. Suppression of each of these six genes in N. benthamiana byvirus-Induced gene silencing resulted in alteration of alkaloid levels.In four cases alkaloid levels were reduced, and in two cases alkaloidlevels were increased. cDNA clones of NbTF1 , NbTF2, NbTF4, NbTF5 ,NbTF6 and NbTF7 were obtained. Constructs for overexpression of thetranscription factors were made and introduced into plant cells. Thedata from the present experiments indicate that the transcription factornucleic acid sequences are useful in the production of plants and plantscells with altered alkaloid levels, in particular altered levels ofnicotinic alkaloids.

These examples are meant to be illustrative only and are not to be readas limiting the present invention.

EXAMPLE 1 Construction of Subtractive cDNA Libraries from Nicotianabenthamiana Roots, EST Sequencing and Selection of Transcription FactorGenes

Nicotine biosynthesis occurs in the roots of Nicotiana species (Dawson,Science 94: 396-397 (1941)) and is induced by insect damage, woundingand the application of jasmonates (Winz and Baldwin, Plant Physiol. 125:2189-2202 (2001)). In order to identify genes encoding transcriptionfactors that control nicotine biosynthesis, we combined expressedsequence tag (EST) sequencing of methyljasmonate (MeJa)-induced roots ofNicotiana benthamiana with functional analysis using virus-induced genesilencing (VIGS) (Liu and Page, Plant Methods 4: 5 (2008)).

Hydroponic Cultivation of Nicotiana benthamiana

Nicotiana benthamiana Domin (Solanaceae) seedlings were grownhydroponically in 0.25× Hoagland's solution supplemented with ironchelate solution and oxygenated using an aquarium bubbler. Roots fromthree-week old plants were sampled before (t=0) and at 1, 4, and 7 hoursafter addition of MeJa to a final concentration of 11 μM. Total RNA wasisolated from 450 mg each of untreated leaves, untreated roots, and acombined MeJa-treated root sample composed of 150 mg roots each from the1, 4 and 7 hour time points using a RNeasy midi kit (Qiagen). Weconstructed three separate subtractive cDNA libraries: NBREL2, with mRNApooled from MeJa-treated roots as tester and untreated root mRNA asdriver; NBLEL3, with mRNA pooled from MeJa-treated roots as tester andleaf mRNA as driver; and NBREL4, with mRNA pooled from MeJa-treatedroots as both tester and driver.

I.A.1.1 Construction of Subtracted VIGS-cDNA Libraries

A PCR-select subtractive cDNA library kit (Clontech) was used for cDNAsynthesis with some modifications. Briefly, about 250 μg of total RNAwas mixed with 300 μl of Oligo (dT)₂₅ Dynabeads (Dynal Biotech) inbinding buffer (20mM Tris-HCl pH 7.5, 1 M LiCl, 2 mM EDTA). After 10 minincubation, the beads were washed three times with washing buffer B(10mM Tris-HCl pH 7.5, 0.15M LiCl, 1 mM EDTA), followed by washing twicewith first strand buffer. The washed beads containing mRNA wereresuspended in 40 μl of cDNA synthesis cocktail (8 μl 5× first strandbuffer, 4 μl 10 mM dNTPs, 24 μl RNase-free water and 4 μl (8U) AMYreverse transcriptase) and incubated at 42° C. for 1.5 hours. The secondstrand synthesis was completed by addition of 120 μl of second strandsynthesis cocktail (32 μl of 5× second strand buffer, 3.2 μl of 10 mMdNTPs, 8 μl of 20× enzyme cocktail and 77 μl RNase free water) andincubation at 16° C. for 2 hours, followed by addition of 4 μl (12U) T4DNA polymerase and further incubation for 30 min. The reaction wasstopped by addition of 20 μl 0.5 M EDTA. The beads were magneticallyseparated, the supernatant removed and the beads resuspended in 500 μlof wash buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl, 1% SDS and10 μg/ml glycogen) and heated at 75° C. for 15 min. The beads were thenwashed three times with wash buffer (5 mM Tris-HCl pH7.5, 0.5 mM EDTA, 1M NaCl and 200 μg/ml BSA), followed by two more washes with RsaI buffer.The beads were resuspended in 84 μl H2O, 10 μl 10× RsaI buffer, 3 μl (30U) RsaI, and incubated at 37° C. overnight. The free cDNA was isolatedby magnetic separation of the beads and was used for adapter ligation,hybridizations and primary PCR as described in the manufacturer'sprotocol. Secondary PCR was performed using primers5′-CGGGATCCTCGAGCGGCCGCCCGGGCAGGT-3′ (BamH1 site underlined) (SEQ ID NO:18) and 5′-CGGAATTCAGCGTGGTCGCGGCCGAGGT-3′ (EcoR1 site underlined) (SEQID NO: 19). The PCR-select amplified cDNA fragments (700 ng) weredigested with EcoRI and BamHI, followed by ligation into a similarlydigested TRV-RNA2 vector, pYL156 (Liu et al., Plant Journal 30: 415-429(2002)). The ligation mixture was electroporated into DH1OB E. colicompetent cells to give primary libraries. These was amplified on agarplates, plasmid DNA isolated and used to transform Agrobacteriumtumefaciens C58 via electroporation. The ligation efficiency asdetermined by colony PCR was 98%.

I.A.1.2 EST Sequencing of Subtracted VIGS-cDNA Library andIdentification of Transcription Factor Candidates

To amplify cDNA inserts for sequencing, PCR was performed using vectorprimers 5′-GTTACTCAAGGAAGCACGATGAG-3′ (SEQ ID NO: 20) and5′-CAGTCGAGAATGTCAATCTCGTAG-3′ (SEQ ID NO: 21) and randomly selected A.tumefaciens colonies as template. The resulting PCR products weresequenced directly using BigDye terminators and the primer5′-GTTACTCAAGGAAGCACGATGAG-3′ (SEQ ID NO: 20). 2016 ESTs were sequencedfrom NBREL2, and 1920 each from NBLEL3 and NBREL4. After removal of poorquality sequences, and combining of the three datasets, we obtained 3480unique transcripts consisting of 606 contigs and 2874 singletons. Thetotal VIGS-EST dataset was annotated via BLASTX comparison to the NCBInon-redundant database.

Using a combination of keyword searching on blastx annotations and blastanalysis with transcription factors sequences, we identified 108putative unique transcripts encoding transcription factors . Theseconsisted of 24 contigs and 84 singletons.

EXAMPLE 2 Screening of Transcription Factors for the Effect on LeafNicotine Accumulation Using VIGS

We used virus-induced gene silencing (VIGS) (Baulcombe, Curr. Opin.Plant Biol. 2: 109-113 (1999); Lu et al., Methods 30: 296-303 (2003)) totest the effect of silencing the candidate transcription factor genes onnicotine biosynthesis.

I.A.1.3 VIGS Silencing of Transcription Factors

VIGS constructs representing different transcription factors were testedfor their ability to alter leaf nicotine levels both before and afterapplication of MeJa to leaves. N. benthamiana plants were grown in soilin a controlled environment chamber with 16 hour/23° days and 8 hour/20°nights under approximately 100 μmol/m²/s light intensity. Cultures of A.tumefaciens C58 containing the TRV-RNA1 plasmid or TRV-RNA2 constructs(pYL156) (both described in Liu et al., Plant Journal 30: 415-429 (2002)were grown overnight at 28° C. After centrifugation, the bacterial cellpellet was resuspended in infiltration buffer containing 1 mM MES (pH5), 10 mM MgCl₂ and 100 μM acetosyringone to OD₆₀₀=1 and allowed tostand at room temperature for 3-6 hours before infiltration. Suspensionsof TRV-RNA1 and pYL279 constructs were mixed 1:1 and infiltrated intothe underside of the upper leaves of 3-4 week old plants using a 1 mlsyringe. Negative control plants were infiltrated with buffer only or aTRV-RNA2 construct containing a non-functional fragment of greenfluorescent protein (TRV-GFP). Plants were grown for 3 weeks before leafnicotine levels in infected N. benthamiana plants were measured usingion-pair HPLC before and five days after application of MeJa (0.1% in a0.1% Tween-20 solution sprayed on all leaf surfaces). A known geneencoding a nicotine biosynthetic enzyme (putrescine N-methyltransferase,PMT) was used as a positive control for VIGS knockdown of nicotinebiosynthesis.

I.A.1.4 Nicotine Analysis by Ion Pair HPLC

Young (˜3-5 cm) N. benthamiana leaves were sampled by excising one halfof a leaf from each plant. After determining fresh weight of the sample,200 μl of zirconium beads and 300 μl of 50 mM citrate buffer pH3:methanol (70:30) were added, the sample as homogenized with aBeadbeater followed by incubation in an ultrasonic bath for 10 min. Theresulting extract was incubated at 4° overnight before centrifugationand filtration (0.45 μm, Spin-X) to clarify the extract. Ion-pair HPLCanalysis was performed on a Waters 2695 separations module equipped witha Waters X-Terra RP18 5 μm 4.6×150 mm with precolumn at a columntemperature of 60°. The isocratic elution system consisted of 80% A:20%B where solvent A consisted of 50 mM citrate, 10 mM octanesulfonic acidpH 3.0 (adjusted with triethylamine) containing 5% methanol and solventB was methanol over 15 min at a flow rate of 1 ml/min. Injection volumewas 20 μl. Nicotine was detected at 261 nm via photodiode arraydetection. Quantification was performed using peak area by comparison toa standard curve (r² 0.999) derived from injection of solutions ofauthentic nicotine ranging in concentration from 1040 μg/ml to 10.4μg/ml.

Of the 108 transcription factors tested, VIGS of four led to reducednicotine levels (NbTF1, NbTF4, NbTFS, NbTF6) and VIGS of two gaveincreased constitutive nicotine levels (NbTF7) or increased levels afterMeJa application (NbTF3) (FIG. 1). Buffer and TRV-GFP control plants hadsimilar nicotine levels, indicating that TRV infection had littleinfluence on nicotine biosynthesis. As expected, the silencing ofputrescine N-methyltransferase, a key enzyme in the nicotine pathway,led to substantial reductions in leaf nicotine.

EXAMPLE 2 Cloning of Full-Length cDNAs for Transcription FactorsAffecting Leaf Nicotine Accumulation

I.A.1.5 Full-length cDNAs were obtained using rapid amplification ofcDNA ends (RACE) PCR.

I.A.1.6 NbTF1

I.A.1.7 5′ and 3′ RACE PCR was used to obtain the full-length cDNAsequence of NbTF1. The full-length NbTF1 transcript was 2313 by inlength encoding an open reading frame (ORF) of 2040 bp. The sequence ofthe NbTF1 gene from N benthamiana is set forth in SEQ ID NO: 1. Thesequence of the NbTF1 open reading frame (ORF) is set forth in SEQ IDNO: 2. The predicted amino acid sequence of N benthamiana NbTF1 is setforth in SEQ ID NO: 3.

I.A.1.8 NbTF3

I.A.1.9 The NbTF3 sequence identified from the EST sequencing was a 295by singleton that was extended via genome walking (Genome Walker kit,Clontech), to yield a 626 by fragment.. Despite the use of 5′ and 3′RACE PCR and further application of genome walking, we did not obtainadditional sequence information for NbTF3. The partial sequence of theNbTF3 gene from N. benthamiana is set forth in SEQ ID NO: 4.

I.A.1.10 NbTF4

I.A.1.11 Genome walking was used to obtain the full-length cDNA sequenceof NbTF4. The open reading frame (ORF) of NbTF4 is 759 bp. The sequenceof the NbTF4 gene is set forth in SEQ ID NO: 5. The NBTF4 ORF is setforth in SEQ ID NO: 6. The predicted amino acid sequence of the Nbenthamiana NbTF4 is set forth in SEQ ID NO: 7.

I.A.1.12 NbTF5

I.A.1.13 Blast searching of a conventional N benthamiana root cDNAlibrary was used to obtain the full-length cDNA clone of NbTF5. Thefull-length NbTF5 gene was 2401 by in length encoding an open readingframe (ORF) of 1971 bp. The sequence of the NbTF5 gene from N.benthamiana is set forth in SEQ ID NO: 8. The NbTF5 ORF sequence is setforth in SEQ ID NO: 9. The predicted amino acid sequence of the N.benthamiana NbTF5 is set forth in SEQ ID NO: 10.

I.A.1.14 NbTF6

I.A.1.15 5′ and 3′ RACE PCR was used to obtain the full-length sequenceof NbTF6. The full-length NbTF6 gene was 958 by in length encoding anopen reading frame (ORF) of 669 bp. The sequence of the NbTF6 gene fromN. benthamiana is set forth in SEQ ID NO: 11. The NbTF6 ORF is set forthin SEQ ID NO: 12. The predicted amino acid sequence of the N.benthamiana NbTF6 is set forth in SEQ ID NO: 13.

I.A.1.16 NbTF7

I.A.1.17 5′ and 3′ RACE PCR and GenomeWalking were used to obtain thefull-length sequence of NbTF7. The full-length NbTF7 gene was 3299 by inlength encoding an open reading frame (ORF) of 2667 bp. The sequence ofthe NbTF7 gene from N. benthamiana is set forth in SEQ ID NO: 14. TheNbTF7 ORF sequence is set forth in SEQ ID NO: 15. The predicted aminoacid sequence of the N. benthamiana NbTF7 is set forth in SEQ ID NO: 16.

The six transcription factors represented several different classes oftranscription factors. These classifications, and the DNA sequence ofthe associated cis-element to which they bind, are shown in Table 1.

TABLE 1 Classification of N. benthamiana transcription factorsAssociated Name Transcription Factor Class cis-element NbTF1Myc, basic helix-loop-helix G-box (bHLH) CACGTG NbTF3Myc, basic helix-loop-helix G-box (bHLH) CACGTG NbTF4Homeodomain leucine zipper NbTF5 Myc, basic helix-loop-helix G-box(bHLH) CACGTG NbTF6 AP2, ethylene-response factor GCC-box AGCCGCC NbTF7B3 domain, auxin response CACCTG factor

EXAMPLE 3 Modifying Alkaloid Biosynthesis in Transgenic Plants

We used stable transformation of N. benthamiana to introduce the sixtranscription factor genes as both sense overexpression constructs (forNbTF1, NbTF4, NbTF5, NbTF6, NbTF7) and RNA interference (RNAi)constructs (for all six transcription factors). Open reading frames (foroverexpression) and cDNA fragments (for RNAi) were amplified using PCRand cloned into the Gateway® entry vector pCR8/GW/TOPO (Invitrogen) orpENTR-D/TOPO (Invitrogen). Overexpression constructs were recombinedinto the Gateway® plant transformation vector pK7WG2 using LR clonase(Invitrogen). Similarly, RNAi constructs were recombined into theGateway® RNAi vector pK7GW1WG2(I). All cloning procedures were performedin E. coli and final, sequence confirmed constructs were transformedinto Agrobacterium tumefaciens C58. Plants were transformed using leafdisc methods adapted from Draper et al. (In: Plant GeneticTransformation and Gene Expression: A Laboratory Manual, pp. 97-144.Draper, J., Scott, R., et al. (eds.), Blackwell Scientific Publications(1988)). Briefly leaf discs excised from mature N. benthamiana plantswere surface sterilized, incubated in Agrobacterium culture containingthe construct of interest and then placed on MS agar plates for two tofour days. The leaf disks are transferred to shoot regeneration agarmedia plus 300 μg/ml timentin and 100 μg/ ml kanamycin. After four andsix weeks shoots that had formed on callus tissue were excised andtransferred to MS+timentin+kanamycin agar plates. After roots haddeveloped, plantlets were transferred to soil to form T0 plants.

Genomic DNA was isolated from each TO plant and the presence or absenceof transgenes was determined using PCR. Primers were designed to annealto transformation vector and the transcription factor construct. TOplants shown to be transgenic by PCR were analyzed using ion-pair HPLCto determine leaf nicotine levels. Nicotine was measured in samplescontaining three leaf discs (˜50 mg FW) and converted to a fresh weightbasis. Wild-types varied between batches of regenerated plants due todifferences in growing conditions.

Silencing NbTF1 via RNAi constructs led to reduction of leaf nicotine inseveral of the transgenic lines as compared to both sense overexpressionand wild-type control plants (FIG. 2). Sense overexpression of NbTF1lead to an increase in leaf nicotine levels in line NbTF1 overexpression6.

Overexpression of NbTF4 led to an increase in leaf nicotine compared towild-type plants, while NbTF4 silencing via RNAi gave reduced levels(FIG. 3).

Overexpression of NbTF5 led to large increases in leaf nicotine levelswhile RNAi silencing of this gene resulted in an almost complete blockin nicotine accumulation (FIG. 4).

Transformation of plants with inverted repeats of segments of NbTF3,NbTF6 or NbTF7 in the plasmid pK7GW1WG2(I) did not result in lines withphenotypes similar to those seen in plants with VIGS of the same gene.This may indicate VIGS was more effective in silencing expression in thecells in which nicotine synthesis occurs.

1-38. (canceled)
 39. A genetically engineered, alkaloid-producing plantwith reduced alkaloid content, wherein the plant comprises a recombinantnucleic acid construct comprising a nucleic acid molecule comprising anucleotide sequence selected from the group consisting of: (a) anucleotide sequence set forth in SEQ ID NO: 8 or SEQ ID NO: 9; (b) anucleotide sequence that encodes a polypeptide having the amino acidsequence set forth in SEQ ID NO: 10; (c) a nucleotide sequence at least90% identical to the nucleotide sequences of (a) or (b), and whichencodes a transcription factor that regulates alkaloid biosynthesis; and(d) a nucleotide sequence that hybridizes under stringent conditions tothe nucleotide sequences of (a), (b), or (c), and which encodes atranscription factor that regulates alkaloid biosynthesis; wherein thenucleotide sequence is operably linked to one or more heterologoussequences.
 40. The genetically engineered plant of claim 39, wherein theplant is a nicotinic alkaloid-producing plant.
 41. The geneticallyengineered plant of claim 40, wherein the plant is a member of a genusselected from the group consisting of Nicotiana, Duboisia, Solanum,Anthocercis, Salpiglessis, Eclipta, and Zinnia.
 42. The geneticallyengineered plant of claim 41, wherein the plant is a decreased-alkaloidNicotiana tabacum plant.
 43. The genetically engineered plant of claim39, wherein the recombinant nucleic acid construct further comprises oneor more of the NBB1, A622, QPT, PMT and MPO genes.
 44. Seeds from thegenetically engineered plant of claim 39, wherein the seeds comprise therecombinant nucleic acid construct.
 45. A product having a reduced levelof an alkaloid comprising the genetically engineered plant of claim 42,or fractions or portions thereof.
 46. The product of claim 45, whereinthe tobacco product is a reduced-nicotine cigarette for smokingcessation comprising one or more alkaloids or alkaloid analogs extractedfrom the genetically engineered plant.
 47. The product of claim 45,wherein the tobacco product is a therapeutic, insecticide or syntheticintermediate comprising one or more alkaloids or alkaloid analogsextracted from the genetically engineered plant.
 48. A method ofproducing the genetically engineered plant of claim 39, wherein themethod comprises reducing an alkaloid in the plant.
 49. The method ofclaim 48, wherein the method of reducing an alkaloid comprisesdown-regulating a transcription factor that positively regulatesalkaloid biosynthesis.
 50. The method of claim 49, wherein thetranscription factor is down-regulated by: (a) introducing into theplant a nucleotide sequence comprising at least 21 consecutivenucleotides of a sequence selected from the group consisting of SEQ IDNO: 8, SEQ ID NO: 9, and a sequence that encodes the amino acid sequenceset forth in SEQ ID NO: 10, wherein the consecutive nucleotides are ineither sense or antisense orientation; and (b) growing the plant underconditions whereby the nucleotide sequence decreases levels of thetranscription factor in the plant as compared to a control plant grownunder similar conditions.
 51. The method of claim 49, wherein thetranscription factor is down-regulated by introducing into a plant cellof the plant a nucleic acid construct that expresses a short interferingRNA that suppresses expression of a gene product encoded by SEQ ID NO: 8or SEQ ID NO:
 9. 52. The method of claim 49, wherein the transcriptionfactor is down-regulated by introducing into a plant cell of the plant anucleic acid construct comprising, in the 5′ to 3′ direction, (a) apromoter operably linked to a heterologous nucleic acid encoding SEQ IDNO: 10 in the sense or antisense orientation, and (b) a terminator. 53.The method of claim 48, wherein reducing an alkaloid comprisesdown-regulating a transcription factor that positively regulatesalkaloid biosynthesis and additionally down-regulating at least one ofNBB1, A622, QPT, PMT and MPO.
 54. The method of claim 53, wherein thetranscription factor is down-regulated by: (a) introducing into theplant a nucleotide sequence comprising at least 21 consecutivenucleotides of a sequence selected from the group consisting of SEQ IDNO: 8, SEQ ID NO: 9, and a sequence that encodes the amino acid sequenceset forth in SEQ ID NO: 10, wherein the consecutive nucleotides are ineither sense or antisense orientation; and (b) growing the plant underconditions whereby the nucleotide sequence decreases levels of thetranscription factor in the plant as compared to a control plant grownunder similar conditions.
 55. The method of claim 53, wherein thetranscription factor is down-regulated by introducing into a plant cellof the plant a nucleic acid construct that expresses a short interferingRNA that suppresses expression of a gene product encoded by SEQ ID NO: 8or SEQ ID NO:
 9. 56. The method of claim 53, wherein the transcriptionfactor is down-regulated by introducing into a plant cell of the plant anucleic acid construct comprising, in the 5′ to 3′ direction, a promoteroperably linked to a heterologous nucleic acid encoding SEQ ID NO: 10 inthe sense or antisense orientation, and a terminator.
 57. The method ofclaim 48, wherein the method comprises: (a) providing a population ofmutated plants; (b) detecting and selecting a target mutated plantwithin the population, wherein the target mutated plant has decreasedexpression of a transcription factor that positively regulates alkaloidbiosynthesis as compared to a control plant; and (c) selectivelybreeding the target mutated plant to produce a population of plantshaving decreased expression of a transcription factor that positivelyregulates alkaloid biosynthesis compared to a population of controlplants.
 58. The method of claim 57, wherein detecting comprises: (a)using primers developed from SEQ ID NO: 8 or SEQ ID NO: 9 to amplifyregions of the transcription factor gene from mutated plants in thepopulation of mutated plants; (b) identifying mismatches between theamplified regions and corresponding regions in a wild-type gene thatlead to decreased expression of a transcription factor that positivelyregulates alkaloid biosynthesis; and (c) identifying the mutated plantthat comprises the mismatches.
 59. The method of claim 48, wherein thealkaloid is a nicotinic alkaloid.
 60. The method of claim 59, whereinthe nicotinic alkaloid is selected from the group consisting ofnicotine, nornicotine, anatabine, anabasine, anatalline,N-methylanatabine, N-methylanabasine, myosmine, anabaseine,formylnornicotine, nicotyrine, and cotinine.